Metagenomic Analysis of RNA Viruses in a Fresh Water Lake
Overview Freshwater lakes and ponds are a distinct ecosystem in which host organisms interact with one another while experiencing varying levels of interference by humans. Freshwater lakes act as a nursery for larvae of many species and serves as a medium in which intra- and interspecies viruses may be spread to various organisms. These viruses include, but are not limited to: Norwalk Virus, Coxsackievirus, Echovirus, and Adenovirus. Experiment Identification of RNA Viruses Samples of the water at Lake Needlewood in Montgomery County, Maryland were collected twice: once in November 2006 and once in June 2007. During each collection process, approximately 70 liters of water were gathered from the surface of the lake, while maintaining a distance of ~5 meters from the shore. Once collected, virions were concentrated using tangential flow filtration (also known as cross-flow filtration). The concentrated virions were then treated with nucleases (DNase I and RNase A) to eliminate free nucleic acids from degraded cells. The RNA was then extracted from the treated cells, amplified, and processed using BLASTX. BLASTX homology was compared to CAMERA non-redundant amino acid database to categorize assemblies of the viral RNA discovered. Analysis of this data revealed the presence of all four types of viruses: ssDNA, dsDNA, ssRNA and dsRNA viruses. Results The sequences collected appeared to be from various viral types that have significant similarities to about 30 known viral families. Due to this large variety of viral types found in these fresh water samples, RNA viruses discovered in the experiment may infect a variety of hosts including plants, insects, fish, domestic animals and humans. Potential Environmental Impact Among the RNA viruses discovered in these lake water samples were a newly discovered dsRNA virus that closely resembled the Banna virus and distant viral relatives of the Israel acute paralysis virus of bees. The Banna virus is endemic to Southwest Asia and belongs to the Reoviridae family of viruses, making it a segmented, non-enveloped, double-stranded RNA virus. This virus is an arbovirus, meaning it is transmitted through arthropod vectors, and therefore mainly travels via mosquitoes. From infected mosquitoes, the Banna virus is primarily transferred to humans - though pigs and cattle have also been infected.This disease causes fever (febrile illness) and occasionally, encephalitis. There is no specific treatment for this infection, so symptoms may only be alleviated until the body's immune system can fight and eliminate the infection. The newly discovered dsRNA virus may possess similar mechanisms and symptoms to the Banna virus based on it's similar functional structures. Israel acute paralysis virus of bees was discovered in 2004, though its origin is unknown. This RNA virus belongs to the Picornaviridae superfamily, thus making it a non-enveloped, positive-stranded RNA viruses with an icosahedral capsid. Based on current studies, this RNA virus affects mitochondrial function most significantly out of all the biological processes; this virus also triggers the immune response system. Evidence suggests that this disease has established itself as a persistent infection in honey bee populations, and is likely spread by both horizontal and vertical transmission pathways. This virus has been linked to colony collapse disorder, a process in which worker bees (specifically from European honeybee colonies) suddenly disappear. It is speculated that since this virus belongs to the Picornaviridae family (which contains the poliovirus causing poliomyelitis - infantile paralysis - in bee larvae) that this particular virus targets the offspring of the population. Based on studies done by the University of Jerusalem, the virus' composition has been determined to be: "sometric particles with a mean diameter of 28 nm, composed of about 20% RNA (single-stranded, positive orientation), 8487 bases in length (without the poly A tail) and carry two large Open Reading Frames (ORF), which is a stretch of nucleotides that encode protein(s), which following translation, are cleaved to the final mature proteins. The virus is encapsulated with four proteins derived from the second ORF." (Beeologics) References Djikeng, A., R. Kuzmickas, N. G. Anderson, and D. J. Spiro. "Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, 29 Sept. 2009. Web. 09 Nov. 2014 . (full text found at PlosOne) Israeli Acute Paralysis Virus: Epidemiology, Pathogenesis and Implications for Honey Bee Health Israeli acute Paralysis Virus